Computational protocol: Detection of quantitative trait loci controlling pre-harvest sprouting resistance by using backcrossed populations of japonica rice cultivars

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Protocol publication

[…] In N-BILs, linkage mapping was performed using version 3.0 of MAPMAKER/EXP (Lander et al. ). The Kosambi map function was used to calculate genetic distances (Kosambi ). QTL analyses were performed using composite interval mapping as implemented by the Zmapqtl program (model 6) provided by version 2.5 of the software package QTL Cartographer (Basten et al. ; Genome-wide threshold values (α = 0.05) were used to detect putative QTLs based on the results of 1,000 permutations.In N-CSSLs, K-CSSLs, and advanced substitution lines, GPs were compared with each recurrent parent, Nipponbare or Koshihikari, by using the Dunnett’s multiple comparison procedure provided by the JMP 6.0 software. QTLs were declared present when GPs were significantly different between each line and the recurrent parents. […]

Pipeline specifications

Software tools MAPMAKER, QTL Cartographer
Application WGS analysis
Organisms Oryza sativa Japonica Group